PMID- 37987851
OWN - NLM
STAT- MEDLINE
DCOM- 20231127
LR  - 20231214
IS  - 1438-7948 (Electronic)
IS  - 1438-793X (Print)
IS  - 1438-793X (Linking)
VI  - 23
IP  - 4
DP  - 2023 Nov 21
TI  - 3'-tRF-Cys(GCA) overexpression in HEK-293 cells alters the global expression 
      profile and modulates cellular processes and pathways.
PG  - 341
LID - 10.1007/s10142-023-01272-0 [doi]
LID - 341
AB  - tRNA fragments (tRFs) are small non-coding RNAs generated through specific 
      cleavage of tRNAs and involved in various biological processes. Among the 
      different types of tRFs, the 3'-tRFs have attracted scientific interest due to 
      their regulatory role in gene expression. In this study, we investigated the role 
      of 3'-tRF-Cys(GCA), a tRF deriving from cleavage in the T-loop of tRNA(CysGCA), 
      in the regulation of gene expression in HEK-293 cells. Previous studies have 
      shown that 3'-tRF-Cys(GCA) is incorporated into the RISC complex and interacts 
      with Argonaute proteins, suggesting its involvement in the regulation of gene 
      expression. However, the general role and effect of the deregulation of 
      3'-tRF-Cys(GCA) levels in human cells have not been investigated so far. To fill 
      this gap, we stably overexpressed 3'-tRF-Cys(GCA) in HEK-293 cells and performed 
      transcriptomic and proteomic analyses. Moreover, we validated the interaction of 
      this tRF with putative targets, the levels of which were found to be affected by 
      3'-tRF-Cys(GCA) overexpression. Lastly, we investigated the implication of 
      3'-tRF-Cys(GCA) in various pathways using extensive bioinformatics analysis. Our 
      results indicate that 3'-tRF-Cys(GCA) overexpression led to changes in the global 
      gene expression profile of HEK-293 cells and that multiple cellular pathways were 
      affected by the deregulation of the levels of this tRF. Additionally, we 
      demonstrated that 3'-tRF-Cys(GCA) directly interacts with thymopoietin (TMPO) 
      transcript variant 1 (also known as LAP2alpha), leading to modulation of its levels. 
      In conclusion, our findings suggest that 3'-tRF-Cys(GCA) plays a significant role 
      in gene expression regulation and highlight the importance of this tRF in 
      cellular processes.
CI  - (c) 2023. The Author(s).
FAU - Karousi, Paraskevi
AU  - Karousi P
AUID- ORCID: 0000-0001-8435-4428
AD  - Department of Biochemistry and Molecular Biology, Faculty of Biology, National 
      and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece.
FAU - Samiotaki, Martina
AU  - Samiotaki M
AUID- ORCID: 0000-0001-9952-0636
AD  - Institute for Bioinnovation, Biomedical Sciences Research Center, "Alexander 
      Fleming", Vari, Greece.
FAU - Makridakis, Manousos
AU  - Makridakis M
AUID- ORCID: 0000-0002-0063-3559
AD  - Center of Systems Biology, Biomedical Research Foundation of the Academy of 
      Athens, Athens, Greece.
FAU - Zoidakis, Jerome
AU  - Zoidakis J
AUID- ORCID: 0000-0002-4557-3430
AD  - Department of Biochemistry and Molecular Biology, Faculty of Biology, National 
      and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece.
AD  - Center of Systems Biology, Biomedical Research Foundation of the Academy of 
      Athens, Athens, Greece.
FAU - Sideris, Diamantis C
AU  - Sideris DC
AUID- ORCID: 0000-0001-6518-0098
AD  - Department of Biochemistry and Molecular Biology, Faculty of Biology, National 
      and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece.
FAU - Scorilas, Andreas
AU  - Scorilas A
AUID- ORCID: 0000-0003-2427-4949
AD  - Department of Biochemistry and Molecular Biology, Faculty of Biology, National 
      and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece.
FAU - Carell, Thomas
AU  - Carell T
AUID- ORCID: 0000-0001-7898-2831
AD  - Department for Chemistry, Institute for Chemical Epigenetics, Ludwig Maximilian 
      University of Munich, Munich, Germany.
FAU - Kontos, Christos K
AU  - Kontos CK
AUID- ORCID: 0000-0002-9935-8461
AD  - Department of Biochemistry and Molecular Biology, Faculty of Biology, National 
      and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece. 
      chkontos@biol.uoa.gr.
LA  - eng
GR  - EMBO Scientific Exchange Grant/European Molecular Biology Organization (EMBO)/
GR  - MIS 5002802/European Union (E.U.) and Greece/
PT  - Journal Article
DEP - 20231121
PL  - Germany
TA  - Funct Integr Genomics
JT  - Functional & integrative genomics
JID - 100939343
RN  - 9014-25-9 (RNA, Transfer)
SB  - IM
MH  - Humans
MH  - HEK293 Cells
MH  - *Proteomics
MH  - *RNA, Transfer/genetics
MH  - Gene Expression Regulation
PMC - PMC10663186
OTO - NOTNLM
OT  - Non-coding RNA
OT  - Post-transcriptional regulation
OT  - Proteomics
OT  - Transcriptomics
OT  - tRNA-derived RNA fragment (tRF)
COIS- Prof. Dr. Christos K. Kontos is an Editor for Functional and Integrative 
      Genomics. The authors have no relevant financial or non-financial interests to 
      disclose.
EDAT- 2023/11/21 12:42
MHDA- 2023/11/27 16:18
PMCR- 2023/11/21
CRDT- 2023/11/21 11:08
PHST- 2023/09/24 00:00 [received]
PHST- 2023/11/14 00:00 [accepted]
PHST- 2023/11/12 00:00 [revised]
PHST- 2023/11/27 16:18 [medline]
PHST- 2023/11/21 12:42 [pubmed]
PHST- 2023/11/21 11:08 [entrez]
PHST- 2023/11/21 00:00 [pmc-release]
AID - 10.1007/s10142-023-01272-0 [pii]
AID - 1272 [pii]
AID - 10.1007/s10142-023-01272-0 [doi]
PST - epublish
SO  - Funct Integr Genomics. 2023 Nov 21;23(4):341. doi: 10.1007/s10142-023-01272-0.